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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacctatcttttaagataatgtttcattgtactaatacagccacttgctccaaagccataatcgctgacattgccgtaccgtgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTCGCCATCAATGGATTCGGACGTATCGGACGCAACTTCGTCCGCTGCTGGC

Basic information

species Physcomitrella patens
transcript PP1S135_21V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S135_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G12900.3 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------------------------------------------------------------gtatgtacctatctttta-agataatgtttcattgtactaatacagccacttgctccaaagccataatcgctgacattgccgtaccgtgaattgcagTCCGCTAGCTCTGGAGC---TAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTCGCCATCAATGGATTCGGACGTATCGGACGCAACTTCGTCCGCTGCTGGC
                                                                                                        | |  | |||||  | |   | || | | ||| | | | || ||||||  || |    | |||||  || |    ||  |   |  ||  ||| ||      |||  ||| |     | ||  |  || |||||||||||||| ||||| ||||||||||| |||||  | || ||  | |||||| |  | || |   
gtgagttcctttttcacccactcctctctattgctcctgtgttatatatcttatggtgcaatcttgtaaactcaagagctgtttcttgtgtctaatgccaccattgtagatctatccatgatgaacaaggctgcatggca-tgat-cagcca--tgatt---aaccatatacgttttttttttctgtctctgtgttgtagATGAGAAGCAATGGTGGATACAGGAAAGGGGTGACCGAGGCCAAGATAAAGGTAGCCATCAATGGGTTCGGTAGGATTGGTAGGAACTTCTTGAGGTGTT---

upper sequence: PP1S135_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ13677 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtacctatcttttaagataatgtttcattgtactaatacagccacttgctccaaagccataatcgctgacattgccgtaccgtgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTCGCCATCAATGGATTCGGACGTATCGGACGCAACTTCGTCCGCTGCTGGC
                |  || ||| ||    | ||    |     | | |  || |   |  | ||    ||   |     |  ||   || |   |  || |   |||||| ||| | || ||  |||||||||||||||| || || ||||||||||| ||| | || || || |||||| |||||||||   
---------------gtttgaaaatcttctcgtctatcgcttttctcccct-ttcta---ctttcattatagatgctatgagagtgtagGTTTCGAGCT-CTGG---TGGAGCCAAGCGCGCTGTTGCCGAGGCCAAGATCAAAGTTGCGATCAATGGATTTGGAAGAATTGGCCGGAACTTCATCCGCTGCT---

upper sequence: PP1S135_21V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ29227 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtacctatcttttaagataatgtttcattgtactaatacagccacttgctccaaagccataatcgctgacattgccgtaccgtgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTCGCCATCAATGGATTCGGACGTATCGGACGCAACTTCGTCCGCTGCTGGC
                   | |      || | |     ||       ||  |       |  | ||    ||   |     |  ||   || |   |  || |   |||||| ||| | || ||  |||||||||||||||| || || ||||||||||| ||| | || || || |||||| |||||||||   
-------------------gtttgaaaatcttcgcgtctatcgcttttctcccctttctactttcattatagatgctatgagagtgtagGTTTCGAGCT-CTGG---TGGAGCCAAGCGCGCTGTTGCCGAGGCCAAGATCAAAGTTGCGATCAATGGATTTGGAAGAATTGGCCGGAACTTCATCCGCTGCT---

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|162158978|gb|FC334006.1|FC334006
EST:     GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
EST: gi|162191328|gb|FC368137.1|FC368137
EST:     GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
EST: gi|162174462|gb|FC350741.1|FC350741
EST:     GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
EST: gi|162196726|gb|FC374665.1|FC374665
EST:     GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
EST: gi|100440888|gb|BY962376.1|BY962376
EST:     GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
EST: gi|208400470|gb|DC908697.1|DC908697
EST:     GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
EST: gi|162229215|gb|FC405302.1|FC405302
EST:     GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
EST: gi|162168479|gb|FC344130.1|FC344130
EST:     GAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: GAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
EST: gi|100378294|gb|BY949779.1|BY949779
EST:     GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
EST: gi|162159248|gb|FC335101.1|FC335101
EST:     ATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: ATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
EST: gi|162186444|gb|FC363000.1|FC363000
EST:     GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
EST: gi|162174672|gb|FC351360.1|FC351360
EST:     GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
EST: gi|162162893|gb|FC338116.1|FC338116
EST:     GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
EST: gi|162179467|gb|FC355467.1|FC355467
EST:     GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: GCAAGCGCTCCGAGGACCTCGCCTCCATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
EST: gi|100384889|gb|BY969624.1|BY969624
EST:     TCGCCTCCATTGTCTCGGCTCAGTCTGCTGTG                         TCCGCTAGTTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC
genomic: TCGCCTCCATTGTCTCGGCTCAGTCTGCTGTGgtatgtacct ... tgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagccacttgctccaaagccataatcgctgacattgccgtaccgtgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTCGCCATCAATGGATTCGGACGTATCGGACGCAACTTCGTCCGCTGCTGGC
                          cgctgac  putative branch site (score: 3)
                     ataat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtacctatcttttaagataatgtttcattgtactaatacagccacttgctccaaagccataatcgctgacattgccgtaccgtgaattgcagTCCGCTAGCTCTGGAGCTAAGAGGGCCGTCACCGAGGCCAAGATCAAGGTCGCCATCAATGGATTCGGACGTATCGGACGCAACTTCGTCCGCTGCTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT